multiruby example: discrepencies in y-position of calibrating crystal

[donald-e-boyce]

There are discrepencies in the y-position of the calibrating crystals in the multiruby example.

The results shown below give the orientation and positions of the same grain given in the three files:

• dexela_id3a_20200130.yml: monolithic
• dexela_id3a_20200130_distorted.yml: monolithic with distortion function
• dexela_id3a_20200130_comp.yml: composite

Each file has a section calibration_crystal, which contains the fitted orientations and positions of the three crystals in the specimen. Each file has three crystals but the order is not the same in all. Individual crystals can be identified by their orientation, and the orientations are in very close agreement. Likewise, the x- and z-positions are very close, but the y-positions vary by over 100 micrometers.

For all three files, the y-position varies across the three cyrstals. In fact, there appears to be a consistent offset. The monolithic with distortion is about 80 um more than the composite, and the monolithic is about 130 more than the composite.

crystals: 0, 0, 1
    orientation:                orientation:                orientation:	     
    - 1.2148784044413221        - 1.215186719556741	    - 1.216154387853489	     
    - 0.6945507909200794        - 0.6951399993864372	    - 0.6968723940137541     
    - 0.765702046701113	        - 0.7652899393752023	    - 0.7641242011231963     
    position:		        position:		    position:		     
    - 0.06060121926310595       - 0.062376192982663094	    - 0.06210286714055197    
    - 0.1312120981443553        - 0.08058718647629351	    - -8.824811070374732e-05 
    - -0.06694059935413639      - -0.06896687021379587	    - -0.06802617226264575   

The same thing happens with all three cyrstals:

crystals: 1, 1, 2
    orientation:                 orientation:                orientation:	   
    - 1.4105172207115466	 - 1.4105340942345905	     - 1.4099410088929247   
    - -0.14336674130145605	 - -0.14348059590076465	     - -0.14100994607869302 
    - -0.37238882282338215	 - -0.3723038198382216	     - -0.3744182154504031  
    position:			 position:		     position:		   
    - 0.016940740257706914	 - 0.017289820066692933	     - 0.01899441270201455  
    - -0.1183857552099456	 - -0.1663676385029688	     - -0.24948708702253838 
    - 0.34767784259162654	 - 0.347969622169141	     - 0.3506372539196996   

and

crystals: 2, 2, 0
    orientation:	         orientation:	             orientation:
    - 0.34356534660437343 	 - 0.3435633536849311        - 0.34336499403802
    - 0.8170405732053853  	 - 0.8168778798606029        - 0.8194611392200433
    - -0.01649123635877074	 - -0.01646827287817391      - -0.01682126887333733
    position:		  	 position:		     position:
    - 0.01052568572502354 	 - 0.009675714272255552      - 0.002650786849134199
    - -0.11080094260256373	 - -0.16062921141263217      - -0.2358059585521713
    - -0.33689416855383947	 - -0.3388488872641141       - -0.34287490726628705

[donald-e-boyce]

GUI gives very close results to command line. A slight difference is that the GUI results give the grains in the same order in all three cases, while the CLI gives the grains permuted in the composite case.

monolithic case, no distortion

Y-positions are: 0.130, -0.120, -0.113

# grain ID    completeness  chi^2         exp_map_c[0]             exp_map_c[1]             exp_map_c[2]             t_vec_c[0]               t_vec_c[1]               t_vec_c[2]               inv(V_s)[0,0]            inv(V_s)[1,1]            inv(V_s)[2,2]            inv(V_s)[1,2]*sqrt(2)    inv(V_s)[0,2]*sqrt(2)    inv(V_s)[0,2]*sqrt(2)    ln(V_s)[0,0]             ln(V_s)[1,1]             ln(V_s)[2,2]             ln(V_s)[1,2]             ln(V_s)[0,2]             ln(V_s)[0,1]           
0             0.811218      1.422900e-03  1.2148478148671364e+00   6.9443358816804379e-01   7.6575914542644186e-01   6.2671421119121287e-02   1.2964170633765248e-01   -6.7226235698291753e-02  9.9985169217289571e-01   9.9992503032023727e-01   9.9983979630260400e-01   9.4935442200785264e-06   -1.4872996099800138e-05  2.7170586584216522e-05   1.4831906572254484e-04   7.4972697263978163e-05   1.6021660923648797e-04   -6.7138399999898282e-06  1.0518483430417920e-05   -1.9214686442374947e-05
1             0.807445      1.395526e-03  1.4105121881312583e+00   -1.4316306499214515e-01  -3.7249659825621861e-01  1.6011412602843583e-02   -1.1967499733276384e-01  3.4938570329741897e-01   1.0000396296736092e+00   1.0001101871543707e+00   1.0000634198214935e+00   1.9146148252641021e-05   -1.7632305719265763e-05  -3.3489565526486471e-05  -3.9628530307613253e-05  -1.1018071224949455e-04  -6.3417641199405291e-05  -1.3537048590186698e-05  1.2467120296556365e-05   2.3678840762983549e-05 
2             0.821173      2.006394e-03  3.4366054170827709e-01   8.1671610173477049e-01   -1.6459938655176795e-02  9.2999006998787451e-03   -1.1294912876874517e-01  -3.3495179416631060e-01  1.0000103589234139e+00   1.0001673451119772e+00   1.0000445502332171e+00   2.2173839143079431e-05   -2.6116699562069509e-05  3.6735564576424863e-05   -1.0358361908633712e-05  -1.6733065115416803e-04  -4.4548947471876347e-05  -1.5677850860401076e-05  1.8466991986520778e-05   -2.5973803830213702e-05

monolithic case, with distortion

Y-positions are: 0.081, -0.168, -0.161

# grain ID    completeness  chi^2         exp_map_c[0]             exp_map_c[1]             exp_map_c[2]             t_vec_c[0]               t_vec_c[1]               t_vec_c[2]               inv(V_s)[0,0]            inv(V_s)[1,1]            inv(V_s)[2,2]            inv(V_s)[1,2]*sqrt(2)    inv(V_s)[0,2]*sqrt(2)    inv(V_s)[0,2]*sqrt(2)    ln(V_s)[0,0]             ln(V_s)[1,1]             ln(V_s)[2,2]             ln(V_s)[1,2]             ln(V_s)[0,2]             ln(V_s)[0,1]           
0             0.811218      5.584546e-04  1.2147625368513131e+00   6.9436466895677340e-01   7.6583205284355615e-01   6.3684973134082223e-02   8.0853762464725989e-02   -6.8430756459234202e-02  9.9988079200181779e-01   9.9986157159335631e-01   9.9985656484645236e-01   -1.6223836722221054e-05  -9.4599669960685616e-06  2.5948560513032588e-06   1.1921512808200997e-04   1.3843805624546180e-04   1.4344552955377382e-04   1.1473595820542510e-05   6.6900748386909808e-06   -1.8350383221052387e-06
1             0.807198      6.082831e-04  1.4105731393000893e+00   -1.4354963716870606e-01  -3.7222939831466750e-01  1.7598190072027810e-02   -1.6751320414887039e-01  3.4980765966802568e-01   1.0000672221622178e+00   1.0000467551855212e+00   1.0000630217184645e+00   -3.4688306995387060e-06  -2.9083820079741578e-06  6.5658116371963783e-06   -6.7219890018659854e-05  -4.6754078747364871e-05  -6.3019727557261725e-05  2.4526943123013671e-06   2.0563970297659241e-06   -4.6424628430509313e-06
2             0.821173      1.089078e-03  3.4363859169607847e-01   8.1662132936819953e-01   -1.6421620598419298e-02  7.7031446121467138e-03   -1.6053767003631877e-01  -3.3663053086770378e-01  1.0000142764463655e+00   1.0001109439925815e+00   1.0000521045487509e+00   7.2115575645867003e-06   -5.4760602180094137e-05  2.6453145354439570e-05   -1.4275419888265861e-05  -1.1093765083541015e-04  -5.2102428732349647e-05  -5.0992876801622896e-06  3.8720355712774057e-05   -1.8704126142491756e-05

composite (8 subpanels) case

Y-positions are: 0, -0.250, -0.240

# grain ID    completeness  chi^2         exp_map_c[0]             exp_map_c[1]             exp_map_c[2]             t_vec_c[0]               t_vec_c[1]               t_vec_c[2]               inv(V_s)[0,0]            inv(V_s)[1,1]            inv(V_s)[2,2]            inv(V_s)[1,2]*sqrt(2)    inv(V_s)[0,2]*sqrt(2)    inv(V_s)[0,2]*sqrt(2)    ln(V_s)[0,0]             ln(V_s)[1,1]             ln(V_s)[2,2]             ln(V_s)[1,2]             ln(V_s)[0,2]             ln(V_s)[0,1]           
0             0.813584      1.505264e-04  1.2161816566834267e+00   6.9690192007734997e-01   7.6410154194902691e-01   6.2143138842418226e-02   -3.4609779429996181e-04  -6.8558087585842573e-02  9.9987194544863511e-01   9.9987063453108993e-01   9.9989219957808995e-01   2.4176730490988093e-05   -6.1950157825451765e-06  6.1464612206658152e-06   1.2806277009297159e-04   1.2937399295573991e-04   1.0780638855236428e-04   -1.7097567080116279e-05  4.3810914759888889e-06   -4.3468013345713309e-06
1             0.814560      1.785075e-04  1.4099536427168908e+00   -1.4099253433955036e-01  -3.7442526022843653e-01  1.9580994644892952e-02   -2.4956695781016178e-01  3.4962768196969457e-01   1.0000710865226068e+00   1.0000223975380844e+00   1.0000798896745122e+00   3.7477558634191444e-05   -1.9350435952065927e-05  -1.9572239993164873e-05  -7.1083806728785876e-05  -2.2396840393531312e-05  -7.9886038810754619e-05  -2.6499185928593930e-05  1.3681608314359754e-05   1.3838835485285551e-05 
2             0.827273      1.469546e-03  3.4380751042130137e-01   8.1923031810682234e-01   -1.6935158491811139e-02  5.9644307686608691e-03   -2.4019448735961146e-01  -3.3412781950350728e-01  1.0000258686505301e+00   1.0001294629246877e+00   1.0000673635369735e+00   -3.5575293427906082e-05  -5.6720340162000786e-05  -3.5878833958799246e-05  -2.5867189906601222e-05  -1.2945390697634645e-04  -6.7360147577499339e-05  2.5153564553787658e-05   4.0105786696329042e-05   2.5368700985190001e-05